Existing inconsistencies

dictyBase / Migration

Entrypoint for dictybase overhaul project

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Existing inconsistencies #1

Open ypandit opened 10 years ago

ypandit commented 10 years ago

Needs to be taken care of during overhaul

trxA/trxB
- Annotations for trxA, trxB not present in the GAF
- However, they show up on EBI GOA with UniProt IDs
Selenocysteine
- Hard-coded residue, with the coordinates.

ypandit commented 10 years ago

For 1 -

~~Write a plugin like AppendncRNA~~
Update DDB_G ID - UniProt mapping. Send it to EBI-GOA
- Once they update, add the missing annotations so that they can be retrieved from QuickGO
- Update dicty-GAF and then submit to GO

ypandit commented 10 years ago

trxA/trxB IEA annotations show up in dictyBase GAF, as of Sept 01, 2013 GAF export

ypandit commented 10 years ago

added manual annotations that got lost back to trxA/B today in P2GO, will hopefully be in next GAF.
selenocysteine solution must be found. - petra

pfey03 commented 10 years ago

GO Annotations in dictyBase: Convert UniProt IDs from GAF (GPAD) back into dicty GENE NAMES, which the unique gene name or sometimes is the ID. This will give best context in 'With' and Col.16 (extension) fields.

pfey03 commented 10 years ago

GO extension Display PomBase is displaying extensions, e.g. http://www.pombase.org/spombe/result/SPBC11B10.09 http://www.pombase.org/spombe/result/SPAC24B11.06c Once relationships for extensions are less in flux we can also think about displaying a nice usable forms instead of some technical sounding relationships like 'has_input'.